How do I flatten a selection of a terrain map?
To flatten a part of your mesh:


Go to edit mode.
Select the bits you want to flatten.
Change the pivot point to "Active Element" through the pivot point menu.

Deselect and reselect an element (vertex/edge/face) that represents the height for your flattened selected. This will set this element as the active element. The entire mesh will be flattened to this height.
Scale to 0 on the Z axis via: S-->Z-->0.



That's it!